A number of things can happen, though I'm not sure exactly what you mean.
Do you mean that the ships will not move at all when given a normal move order, or will not go through a wormhole when you tell them to?
In the first case, it could be engine damage from stuff that causes it; if the second case it could be a black hole machine.
There are also paralyzing weapons and emps that can render a ship totally unresponsive for a period of time.